TY  - JOUR
AV  - restricted
A1  - Krishnan, J
A1  - Athar, F
A1  - Swaroopa Rani, T
A1  - Mishra, R K
TI  - Simple sequence repeats showing ?length preference? have regulatory functions in humans
UR  - https://doi.org/10.1016/j.gene.2017.07.022
JF  - Gene
SN  - 0378-1119
PB  - Elsevier
N1  - We thank Gary Felsenfeld for his kind gift of boundary assay
plasmid and S. Krishnan for the barrier assay plasmid. We acknowledge
financial support of Council of Scientific and Industrial Research (CSIR)
through Network grants (BSC0118 and BSC0121).
N2  - Simple sequence repeats (SSRs), simple tandem repeats (STRs) or microsatellites are short tandem repeats of 1?6 nucleotide motifs. They are twice as abundant as the protein coding DNA in the human genome and yet little is known about their functional relevance. Analysis of genomes across various taxa show that despite the instability associated with longer stretches of repeats, few SSRs with specific longer repeat lengths are enriched in the genomes indicating a positive selection. This conserved feature of length dependent enrichment hints at not only sequence but also length dependent functionality for SSRs. In the present study, we selected 23 SSRs of the human genome that show specific repeat length dependent enrichment and analysed their cis-regulatory potential using promoter modulation, boundary and barrier assays. We find that the 23 SSR sequences, which are mostly intergenic and intronic, possess distinct cis-regulatory potential. They modulate minimal promoter activity in transient luciferase assays and are capable of functioning as enhancer-blockers and barrier elements. The results of our functional assays propose cis-gene regulatory roles for these specific length enriched SSRs and opens avenues for further investigations.
KW  - Simple sequence repeats
KW  -  Microsatellites
KW  -  Simple tandem repeats
KW  -  Cis-regulatory activity
KW  -  Gene regulation
KW  -  Boundary elements
KW  -  Barrier elements
KW  -  SSRs
KW  -  STRs
KW  -  QTLs
KW  -  human cell lines
Y1  - 2017/08/10/
SP  - 156
ID  - icrisat10337
EP  - 161
VL  - 628
ER  -